The use of antimicrobials as growth promoters (AGPs) has become common in the aquaculture industry. As a consequence of this practice, questions challenging both the safety and quality of farmed Atlantic salmon (Salmo salar) are emerging. The microbiota of Atlantic salmon are predominantly determined by bacteria present in their environment as well as their diet, and thus feeding Atlantic salmon AGP’s may affect the presence of some bacteria and confer resistance. In Canada, only tetracyclines are allowed for use in the aquaculture industry. Here, we surveyed the cultivable flora associated with both farmed and wild Atlantic salmon and assessed antimicrobial resistance (AMR) within these bacterial communities and isolates. Samples (taken from the mouth, gills, skin, intestinal mucosa, and intestinal contents) were first plated on growth media with or without added chlortetracycline (1 μg/mL). Cultured bacteria were then typed using denaturing gradient gel electrophoresis (DGGE) and partial 16S rRNA gene sequencing. Identification was based on 16S rRNA sequence homology of sequences within the Ribosomal Database Project. Community DNA from wild and farmed salmon was also compared using DGGE. The presence of tetracycline resistance genes was assessed by polymerase chain reaction (PCR) using primer sets specific for 19 known tetracycline resistance genes. In total 173 bacterial species were isolated and typed using DGGE. The five samples from wild salmon consisted of 64 unique species, whereas only 17 species were cultivated from farmed salmon. Overall, 80% of isolates from the wild salmon and 25% of isolates from the farmed salmon carried genes encoding for resistance to tetracycline. In farmed salmon the resistance genes tetW>tetS>tetM, tetO>tetT>tetQ, tetZ>tetG were identified, whereas in wild salmon tetW>tetS were found. Though there was more than three times the presence of tetracycline resistance genes in wild salmon, this may not be an accurate representation of the whole community resistance as some genes present may not be expressed or functional. This study is based on cultivable bacteria only. Until uncultivable bacteria are also tested for resistance genes a true comparison of resistance within each community cannot be made.

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